Sat Oct 15 13:59:08 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 13:59:09 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5126876 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 0.5126876 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4102 net assigned charge : -1.099974 assigned positive charge : 644.0983 centred at (gu) : 90.12227 90.60038 87.67840 assigned negative charge : -645.2022 centred at (gu) : 89.98483 90.65408 87.80064 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7095 nv = 96 ne = 84 npr = 87976 no. pairs analyzed = 87976 no. exposed pairs = 5651 no. arc points = 38970 no. surface atoms = 1878 nbur = 2426 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 272 mr = 3614 m= 0 mr = 9 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 3744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3705 ## 547 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 9568 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2869781E-10 -1.8502874E-10 midg,1,midg; midg,igrid,midg 9.4926116E-11 -1.8990445E-10 1,midg,midg; igrid,midg,midg -3.6822162E-10 3.2976410E-10 gauss-seidel spectral radius is 0.9805085 estimated iterations to convergence 59 setup time was (sec) 0.7600000 now iterating at: 13:59:11 rms-change max change #iterations 6.5821432E-02 10.92624 at 10iterations 3.9003550E-03 0.5897465 at 20iterations 2.7533292E-04 4.2049408E-02 at 30iterations 5.2328742E-05 6.7844391E-03 at 40iterations 1.6956057E-05 2.1581650E-03 at 50iterations finished qdiffx linear iterations at : 13:59:24 total time elapsed so far: 5.290000 # loops : 50 mean,max change (kT/e) : 1.6956057E-05 2.1581650E-03 energy calculations done at 5.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.530000 DelPhi exited at 13:59:26 5.538u 0.494s 0:16.93 35.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 13:59:28 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.538063 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 1.538063 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4102 net assigned charge : -1.099974 assigned positive charge : 644.0983 centred at (gu) : 90.36591 91.79980 83.03393 assigned negative charge : -645.2022 centred at (gu) : 89.95386 91.96182 83.40160 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22686 mr = 54301 m= 2008 mr = 14659 m= 44 mr = 791 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.6700000 number of dielectric boundary points 35101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 512 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 30918 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5126876 object centre at (A) : 10.66950 -0.3594999 30.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1888904E-03 -1.4306783E-02 midg,1,midg; midg,igrid,midg -4.4059274E-03 -1.0077624E-02 1,midg,midg; igrid,midg,midg -4.1604307E-03 8.6527942E-03 gauss-seidel spectral radius is 0.9980819 estimated iterations to convergence 181 setup time was (sec) 0.9700000 now iterating at: 13:59:34 rms-change max change #iterations 3.630288 179.3423 at 10iterations 1.466627 48.97771 at 20iterations 0.5978073 20.72461 at 30iterations 0.2428339 8.226794 at 40iterations 9.8605506E-02 3.227916 at 50iterations 4.0163025E-02 1.311055 at 60iterations 1.6398160E-02 0.5226049 at 70iterations 6.7097871E-03 0.2315903 at 80iterations 2.7495723E-03 9.9807262E-02 at 90iterations 1.1397144E-03 3.8505554E-02 at 100iterations 4.8216796E-04 1.6161919E-02 at 110iterations 2.1526996E-04 7.7800751E-03 at 120iterations finished qdiffx linear iterations at : 13:59:59 total time elapsed so far: 12.40000 # loops : 120 mean,max change (kT/e) : 2.1526996E-04 7.7800751E-03 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 14:00:01 12.581u 0.486s 0:33.50 38.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 14:00:04 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4304 !!! WARNING: HEM 819 has a net charge of -3.4000 !!! WARNING: FE 2 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.307094 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -15.92800 37.26700 ymin,ymax (A): -32.02800 31.30900 zmin,zma (A): -3.858000 65.58000 x,y,z range (A): 53.19500 63.33700 69.43800 scale (grids/A): 2.307094 object centre (A): 10.66950 -0.3594999 30.86100 number of atom coordinates read : 4304 total number of charged atoms : 4102 net assigned charge : -1.099974 assigned positive charge : 644.0983 centred at (gu) : 90.54832 92.69938 79.55055 assigned negative charge : -645.2022 centred at (gu) : 89.93063 92.94262 80.10233 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 186950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38970 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 81776 mr = 133862 m= 20203 mr = 62976 m= 2784 mr = 14041 m= 135 mr = 1626 m= 0 mr = 24 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 422 time to turn everything in is 1.730000 number of dielectric boundary points 79319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 32755 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.538063 object centre at (A) : 10.66950 -0.3594999 30.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1568342 -0.2996728 midg,1,midg; midg,igrid,midg -0.1156092 -0.2303908 1,midg,midg; igrid,midg,midg -5.4674845E-02 0.1179080 gauss-seidel spectral radius is 0.9991431 estimated iterations to convergence 270 setup time was (sec) 2.130000 now iterating at: 14:00:09 rms-change max change #iterations 9.839670 292.4771 at 10iterations 5.607415 135.6864 at 20iterations 3.171058 74.53114 at 30iterations 1.780735 43.69453 at 40iterations 0.9987858 23.53418 at 50iterations 0.5572777 12.07667 at 60iterations 0.3106672 7.024893 at 70iterations 0.1728069 3.329161 at 80iterations 9.5786430E-02 2.129553 at 90iterations 5.3039007E-02 1.141821 at 100iterations 2.9382218E-02 0.7161980 at 110iterations 1.6269719E-02 0.3393898 at 120iterations 8.9791557E-03 0.1858540 at 130iterations 4.9530836E-03 0.1054916 at 140iterations 2.7373761E-03 5.6919813E-02 at 150iterations 1.5150106E-03 2.8536797E-02 at 160iterations 8.3629368E-04 1.6487122E-02 at 170iterations 4.6218964E-04 9.1609955E-03 at 180iterations finished qdiffx linear iterations at : 14:00:52 total time elapsed so far: 20.89000 # loops : 180 mean,max change (kT/e) : 4.6218964E-04 9.1609955E-03 energy calculations done at 20.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.05000 DelPhi exited at 14:00:53 21.057u 0.620s 0:49.59 43.6% 0+0k 0+0io 0pf+0w